[Bioc-devel] Error: file larger than 5 Mb.

[Martin Morgan]

Good news, the file is in AnnotationHub and can be used from there. 
There is a download cost the first time but not subsequently.

library(AnnotationHub)
hub = AnnotationHub()
query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")

## note 'AH' number, then...
gtf = hub[["AH63797"]]

Need the path rather than the imported path? use cache(hub["AH63797"]) 
instead.

Martin

On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
> To generate mouse.rda, I used:
> 
> library(rtracklayer)
> mouse <- readGFF("
> ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
> ")
> 
> And then I saved the object as mouse.rda
> 
> 
> On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk <khomtchoukmed using gmail.com>
> wrote:
> 
>> Here it is:
>> https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
>>
>>
>> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey <stvjc using channing.harvard.edu>
>> wrote:
>>
>>> (resending with reply all -- please reply to this one)
>>>
>>> Can you say some more about the content of the file?  Perhaps it can be
>>> placed in ExperimentHub.  "mouse.rda" is not very descriptive.  is it
>>> in your github repo?
>>>
>>>
>>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
>>> khomtchoukmed using gmail.com> wrote:
>>>
>>>> I need to include an important .rda file in the /data folder of my
>>>> Bioconductor package.  However, this .rda file exceeds 5 Mb in size.  Do
>>>> I
>>>> have any other options besides for deleting it?
>>>>
>>>> bohdankhomtchouk$ git push origin master
>>>>
>>>> Counting objects: 65, done.
>>>>
>>>> Delta compression using up to 8 threads.
>>>>
>>>> Compressing objects: 100% (65/65), done.
>>>>
>>>> Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
>>>>
>>>> Total 65 (delta 30), reused 0 (delta 0)
>>>>
>>>> remote: Error: file larger than 5 Mb.
>>>>
>>>> remote:
>>>>
>>>> remote:     File name: 'data/mouse.rda'
>>>>
>>>> remote:     File size: 12.9 Mb
>>>>
>>>> remote:
>>>>
>>>> remote: Please see Biocondcutor guidelines
>>>>
>>>> remote: https://bioconductor.org/developers/package-guidelines/
>>>>
>>>> remote:
>>>>
>>>> To git.bioconductor.org:packages/geneXtendeR
>>>>
>>>>   ! [remote rejected] master -> master (pre-receive hook declined)
>>>>
>>>> error: failed to push some refs to 'git using git.bioconductor.org:
>>>> packages/geneXtendeR'
>>>>
>>>> --
>>>> Bohdan Khomtchouk, Ph.D.
>>>> AHA Postdoctoral Fellow, Gozani & Assimes Labs
>>>> Department of Biology & Department of Medicine
>>>> Division of Cardiovascular Medicine
>>>> Stanford University
>>>> Stanford, CA 94305
>>>> https://profiles.stanford.edu/bohdan-khomtchouk
>>>>
>>>>
>>>> CONFIDENTIALITY NOTICE: Information contained in this me...{{dropped:9}}
>>>>
>>>> _______________________________________________
>>>> Bioc-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
>>> The information in this e-mail is intended only for t...{{dropped:17}}
> 
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>